Pyknot: A pymol tool for the discovery and analysis of knots in proteins

Bioinformatics

Volumn 28, Issue 15, 2012, Pages 2069-2071

  Lua, Rhonald C ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN FOLDING;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SOFTWARE;

EID: 84865154095     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts299     Document Type: Article

References (19)

1. Bolinger,D. et al. (2010)AStevedore's protein knot. PLoS Comput. Biol., 6, e1000731.
2. Khatib,F. et al. (2009) Pokefind: a novel topological filter for use with protein structure prediction. Bioinformatics, 25, i281-i288.
3. Khatib,F. et al. (2006) Rapid knot detection and application to protein structure prediction. Bioinformatics, 22, e252-e259. 2070 PyKnot Kolesov,G. et al. (2007) Protein knot server: detection of knots in protein structures. Nucleic Acids Res., 35 (Web Server issue), W425-W428.
4. Knot Kolesov,G. et al. (2007) Protein knot server: detection of knots in protein structures. Nucleic Acids Res., 35 (Web Server issue), W425-W428
5. Koniaris,K. and Muthukumar,M. (1991) Knottedness in ring polymers. Phys. Rev. Lett., 66, 2211-2214.
6. Lai,Y.L. et al. (2007) pKNOT: the protein KNOT web server. Nucleic Acids Res., 35 (Web Server issue), W420-W424.
7. Lua,R.C. et al. (2004) Fractal and statistical properties of large compact polymers: a computational study. Polymer, 45, 717-731.
8. Lua,R.C. and Grosberg,A.Y. (2006) Statistics of knots, geometry of conformations, and evolution of proteins. PLoS Comput. Biol., 2, e45.
9. Moore,N.T. et al. (2004) Topologically driven swelling of a polymer loop. Proc. Natl Acad. Sci. USA, 101, 13431-13435.
10. Polyak,M. and Viro,O. (1994) Gauss diagram formulas for Vassiliev invariants. Int. Math. Res. Notes, 11, 445-453.
11. Sayre,T.C. et al. (2011) Protein stabilization in a highly knotted protein polymer. Protein Eng. Des. Sel., 24, 627-630.
12. Schmidberger,J.W. et al. (2008) The crystal structure of DehI reveals a new alphahaloacid dehalogenase fold and active-site mechanism. J. Mol. Biol., 378, 284-294.
13. Sulkowska,J.I. et al. (2009) Dodging the crisis of folding proteins with knots. Proc. Natl Acad. Sci. USA, 106, 3119-3124.
14. Sulkowska,J.I. et al. (2008) Stabilizing effect of knots on proteins. Proc. Natl Acad. Sci. USA, 105, 19714-19719.
15. Taylor,W.R. (2000) A deeply knotted protein structure and how it might fold. Nature, 406, 916-919.
16. Taylor,W.R. (2007) Protein knots and fold complexity: some new twists. Comput. Biol. Chem., 31, 151-162.
17. Virnau,P. et al. (2006) Intricate knots in proteins: function and evolution. PLoS Comput. Biol., 2, e122.
18. Vologodskii,A. et al. ( 1974) Problem of knots in statistical mechanics of polymer chains. Sov. Phys. JETP, 39, 1059-1063.
19. Wagner,J.R. et al. (2005) A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature, 438, 325-331.